setup-r-deps: replace github-token param with GITHUB_PAT env var (#…

…262) Fix the issue when private repos cannot be accessed: https://github.com/insightsengineering/citril/actions/runs/11717635984/job/32642879518?pr=464 - `github-token` was not used and removed in a companion PR: insightsengineering/setup-r-dependencies#17 - set up `GITHUB_ENV` on setup-r-deps use --------- Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
insightsengineering · Nov 7, 2024 · d45f912 · d45f912
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commit d45f912
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Showing 8 changed files with 18 additions and 9 deletions.
diff --git a/.github/workflows/bioccheck.yaml b/.github/workflows/bioccheck.yaml
@@ -159,9 +159,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Run BiocCheck ☣️

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
@@ -437,9 +437,10 @@ jobs:
           env.deps_installation_method == 'setup-r-dependencies'
           && inputs.install-deps-from-package-repositories == ''
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
           skip-desc-branch: ${{ inputs.skip-desc-branch }}
           skip-desc-dev: ${{ inputs.skip-desc-dev }}

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -231,9 +231,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install R package 🚧

diff --git a/.github/workflows/revdepcheck.yaml b/.github/workflows/revdepcheck.yaml
@@ -92,10 +92,11 @@ jobs:
 
       - name: Install dependencies
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-desc-branch: true
-          github-token: ${{ steps.github-token.outputs.token }}
 
       - name: revdepcheck 🔄
         id: revdepcheck

diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
@@ -97,10 +97,11 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
-          github-token: ${{ steps.github-token.outputs.token }}
           restore-description: false
           install-quarto: "false"
 
@@ -149,10 +150,11 @@ jobs:
           job-config: ${{ matrix.config.job-config }}
 
       - uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
           skip-install: true
-          github-token: ${{ steps.github-token.outputs.token }}
           restore-description: false
           install-quarto: "false"
 

diff --git a/.github/workflows/roxygen.yaml b/.github/workflows/roxygen.yaml
@@ -153,9 +153,10 @@ jobs:
         if: >-
           env.deps_installation_method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Generate man pages 📄

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -244,9 +244,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}
 
       - name: Install R package 🚧

diff --git a/.github/workflows/validation.yaml b/.github/workflows/validation.yaml
@@ -148,9 +148,10 @@ jobs:
         if: >-
           inputs.deps-installation-method == 'setup-r-dependencies'
         uses: insightsengineering/setup-r-dependencies@v1
+        env:
+          GITHUB_PAT: ${{ steps.github-token.outputs.token }}
         with:
           lookup-refs: ${{ inputs.lookup-refs }}
-          github-token: ${{ steps.github-token.outputs.token }}
           repository-path: ${{ env.package_subdirectory }}
 
       - name: Build report 🏗